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Purpose

This document will run through the analysis requested by Jess for the PT paper.

The resulting D13 and D13+14 pooled replicate libraries resolved 19,956 and 15,852 individual cell transcriptomes per timepoint, respectively. tSNE plots showed the resolution of distinct clusters for both D13 monolayers and resulting PT-enhanced (D13+14) organoids (Figure 3B – Jess still to add).

To confirm whether the enhanced protocol improves the specification, patterning, and maturation of kidney cell types, D13 and D13+14 samples were directly compared to monolayers and organoids arising from our standard organoid protocol (D7 and D7+14[?]), as well as normal human (fetal?) kidney, using the R package DevKidCC (Wilson et al 2021) (Figure 3C-D – sean to add proportion plots).

Load extended diff datasets

Run DevKidCC on required data

What data would we compare it do? warum nicht alle?

Note the lack of HOXD11 in Low et al, seemingly the same time point (although not monolayer)

For the PT genes, there is high expression of CUBN and SLC3A1, lower (but still clearly present) expression of LRP2, SLC47A1 and HNF4A, while ACE2 is clearly expressed albeit lowly and in fewer cells.

This may be where imputation with MAGIC could come in handy. Their original paper said it had utility in filling out gene expression that is likely there but not collected, particularly with lower expressing genes, allowing for better head to head plotting (i.e. can do an ACE2 vs PT markers plot and show correlation between them).

Jess Wish List

NPC (Self-Renewing)

NPC (Committed)

NPC (Primed)

Metanephric HOX

Proximal Tubule